Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi

Abstract

The members of the Ras-like superfamily of small GTP-binding proteins are molecular switches that are in general regulated in time and space by guanine nucleotide exchange factors and GTPase activating proteins. The Ras-like G-proteins Ras, Rap and Ral are regulated by a variety of guanine nucleotide exchange factors that are characterized by a CDC25 homology domain. Here we study the evolution of the Ras pathway by determining the evolutionary history of CDC25 homology domain coding sequences. We identified CDC25 homology domain coding sequences in animals, fungi and a wide range of protists, but not in plants. This suggests that the CDC25 homology domain originated in or before the last eukaryotic ancestor but was subsequently lost in plant. We provide evidence that at least seven different ancestral Ras guanine nucleotide exchange factors were present in the ancestor of fungi and animals. Differences between present day fungi and animals are the result of loss of ancestral Ras guanine nucleotide exchange factors early in fungal and animal evolution combined with lineage specific duplications and domain acquisitions. In addition, we identify Ral guanine exchange factors and Ral in early diverged fungi, dating the origin of Ral signaling back to before the divergence of animals and fungi. We conclude that the Ras signaling pathway evolved by gradual change as well as through differential sampling of the ancestral CDC25 homology domain repertoire by both fungi and animals. Finally, a comparison of the domain composition of the Ras guanine nucleotide exchange factors shows that domain addition and diversification occurred both prior to and after the fungal–animal split.